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spec stage 2 clutch has a sticker on the back that says flywheel side but Im wondering if its wrong cause the trans wont go in all the way and I found that the input shaft cover or retainer( whatever you want to call it is hitting the clutch when its pushed in. What does the side of the disk look like thats suppose to face the flywheel? The flat side right? The puck side faces the tranny? I dont trust this little sticker especially since I bought it from someone that already installed it and I dotn know what he did with it. Also are the dowel pins critical cause im missing all mine. Really dont want to pull the bitch back apart but I will if I have to. The dowel pin holes are lined up with the holes on the pressure plate( all 3) just didnt have the new dowel pins to install and the holes in the flywheel are much bigger then the ones in the pressure plate and i didnt want to drill the holes out since something about that dont seem right

Dowl pins are very, very critical, Period.

As for your other problem, most times the flat side of the clutch goes toward the engine, but there are exceptions to every rule.